id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17684 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : { ""HEALTH_FEATURE_AVAILABILITY"" : ""65a855f5f087695cfac03d1f"" }, ""deploymentId"" : 240000187 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/ChimeraX/D398.cxs Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened P34_J608_004.cmap as #5, grid size 256,256,256, pixel 0.932, shown at level 0.506, step 1, values float32 Opened P49_J393_003.cmap as #6, grid size 256,256,256, pixel 0.932, shown at level 0.411, step 1, values float32 Opened P34_J1433.cmap as #7, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 0 as #9.1, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 1 as #9.2, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 2 as #9.3, grid size 256,256,256, pixel 0.932, shown at level 0.562, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 3 as #9.4, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened P34_J608_004.cmap 0 as #10.1, grid size 256,256,256, pixel 0.932, shown at level 0.506, step 1, values float32 Opened P34_J608_004.cmap 1 as #10.2, grid size 256,256,256, pixel 0.932, shown at level 0.506, step 1, values float32 Opened P34_J608_004.cmap 2 as #10.3, grid size 256,256,256, pixel 0.932, shown at level 0.362, step 1, values float32 Opened P49_J393_003.cmap 0 as #11.1, grid size 256,256,256, pixel 0.932, shown at level 0.411, step 1, values float32 Opened P49_J393_003.cmap 1 as #11.2, grid size 256,256,256, pixel 0.932, shown at level 0.411, step 1, values float32 Opened P49_J393_003.cmap 2 as #11.3, grid size 256,256,256, pixel 0.932, shown at level 0.201, step 1, values float32 Opened P34_J1433.cmap 0 as #12.1, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 1 as #12.2, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 2 as #12.3, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 3 as #12.4, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 4 as #12.5, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 5 as #12.6, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 0 as #13.1, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 1 as #13.2, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 2 as #13.3, grid size 256,256,256, pixel 0.932, shown at level 0.157, step 1, values float32 Opened P34_J1433.cmap 3 as #13.4, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Log from Wed Dec 11 15:01:23 2024 Startup Messages --- warnings | Data format provider 'LAMMPS coordinates' supplied unknown keywords with format description: {'default_for': '.data'} Data format provider 'LAMMPS trajectory' supplied unknown keywords with format description: {'default_for': '.dump'} Data format provider 'LAMMPS coordinates' supplied unknown keywords with format description: {'default_for': '.data'} Data format provider 'LAMMPS trajectory' supplied unknown keywords with format description: {'default_for': '.dump'} Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open D:/183/183-map/183-0708-PDB/ACh/ACh-cryosparc_P34_J1670_map_2.72.mrc Opened ACh-cryosparc_P34_J1670_map_2.72.mrc as #1, grid size 256,256,256, pixel 0.932, shown at level 0.189, step 1, values float32 > open ""D:/183/183-map/183-0708-PDB/ACh/VAChT-ACh -all.pdb"" Chain information for VAChT-ACh -all.pdb #2 --- Chain | Description A | No description available > volume #1 level 0.6025 > set bgColor white > open D:/183/183-map/183-0708-PDB/apo/apo- > cryosparc_P34_J608_004_volume_map_sharp-resample.mrc Opened apo-cryosparc_P34_J608_004_volume_map_sharp-resample.mrc as #3, grid size 256,256,256, pixel 0.932, shown at level 0.195, step 1, values float32 > open D:/183/183-map/183-0708-PDB/apo/VAChT-apo.pdb Chain information for VAChT-apo.pdb #4 --- Chain | Description B | No description available > volume #3 level 0.4207 > open ""D:/183/183-map/183-0708-PDB/ph=5.5/vop resample-918-3.3-ph5.5.mrc"" Opened vop resample-918-3.3-ph5.5.mrc as #5, grid size 256,256,256, pixel 0.932, shown at level 0.151, step 1, values float32 > open D:/183/183-map/183-0708-PDB/ph=5.5/0813-apo-coot-13.pdb Chain information for 0813-apo-coot-13.pdb #6 --- Chain | Description A | No description available > volume #5 level 0.3406 > open D:/183/183-map/183-0708-PDB/vesamicol/Vesamicol- > cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc Opened Vesamicol-cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc as #7, grid size 256,256,256, pixel 0.932, shown at level 0.0508, step 1, values float32 > open D:/183/183-map/183-0708-PDB/vesamicol/0812-VSM.pdb Chain information for 0812-VSM.pdb #8 --- Chain | Description A | No description available > volume #5 level 0.6636 > volume #7 level 0.3121 > cartoon style width 0.7 > transparency 60 cartoons > hide #!8 models > show #!8 models > hide #!6 models > hide #!4 models > hide #!2 models > hide #!8 models > show #!8 models > close #8 > open D:/183/183-map/183-0708-PDB/vesamicol/pdb-load/vsm_PDB-coot-0.pdb Chain information for vsm_PDB-coot-0.pdb #8 --- Chain | Description A | No description available > close #8 > open D:/183/183-map/183-0708-PDB/vesamicol/pdb-load/vsm_PDB.pdb Chain information for vsm_PDB.pdb #8 --- Chain | Description A | No description available > show #!6 models > hide #!8 models > show #!8 models > hide #!7 models > select add #6 3037 atoms, 3112 bonds, 1 pseudobond, 404 residues, 2 models selected > select subtract #6 Nothing selected > select add #8 3068 atoms, 3146 bonds, 1 pseudobond, 406 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.98754,-0.10604,-0.11624,24.986,0.1012,0.99376,-0.046825,-4.9074,0.12048,0.034479,0.99212,-15.408 > view matrix models > #8,-0.96306,0.2136,-0.16397,201.68,-0.22098,-0.27893,0.93454,55.656,0.15388,0.93626,0.31583,-39.911 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.96306,0.2136,-0.16397,217.04,-0.22098,-0.27893,0.93454,64.528,0.15388,0.93626,0.31583,-35.804 > color #6 #00aaff66 > cartoon style width 2 > select add #6 6105 atoms, 6258 bonds, 2 pseudobonds, 810 residues, 4 models selected > view matrix models > #6,1,0,0,12.821,0,1,0,-7.4184,0,0,1,4.2268,#8,-0.96306,0.2136,-0.16397,229.86,-0.22098,-0.27893,0.93454,57.11,0.15388,0.93626,0.31583,-31.578 > view matrix models > #6,1,0,0,7.2454,0,1,0,-4.4674,0,0,1,3.2543,#8,-0.96306,0.2136,-0.16397,224.28,-0.22098,-0.27893,0.93454,60.061,0.15388,0.93626,0.31583,-32.55 > select subtract #8 3037 atoms, 3112 bonds, 1 pseudobond, 404 residues, 2 models selected > select subtract #6 Nothing selected > select add #8 3068 atoms, 3146 bonds, 1 pseudobond, 406 residues, 2 models selected > view matrix models > #8,-0.96306,0.2136,-0.16397,181.78,-0.22098,-0.27893,0.93454,68.798,0.15388,0.93626,0.31583,-56.806 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.97565,0.088717,-0.20059,200.13,-0.17507,-0.86592,0.46854,175.82,-0.13213,0.49225,0.86037,-39.339 > view matrix models > #8,-0.88548,0.0056539,-0.46464,227.94,0.34126,-0.67073,-0.65853,223.27,-0.31537,-0.74168,0.59199,137.97 > view matrix models > #8,-0.95761,-0.21089,-0.19624,229.08,0.28585,-0.61124,-0.73802,231.48,0.035694,-0.76283,0.64561,97.486 > view matrix models > #8,-0.93496,0.23324,-0.26728,187.97,0.27583,0.95178,-0.13431,3.7536,0.22307,-0.1993,-0.95421,192.21 > hide #!6 models > show #!2 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.93052,0.228,-0.2866,190.14,0.27476,0.95203,-0.13472,3.8846,0.24214,-0.20411,-0.94853,190.1 > view matrix models > #8,-0.94206,0.24257,-0.23169,183.88,0.27781,0.9513,-0.13361,3.5205,0.18799,-0.19024,-0.96357,195.96 > view matrix models > #8,-0.92605,0.22303,-0.30445,192.13,0.27377,0.95226,-0.13512,4.0084,0.25978,-0.20848,-0.9429,188.09 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.92605,0.22303,-0.30445,231.05,0.27377,0.95226,-0.13512,2.8097,0.25978,-0.20848,-0.9429,212.04 > hide #!2 models > show #!7 models > ui tool show ""Fit in Map"" > fitmap #8 inMap #7 Fit molecule vsm_PDB.pdb (#8) to map Vesamicol- cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) using 3068 atoms average map value = 0.05745, steps = 112 shifted from previous position = 2.29 rotated from previous position = 7.01 degrees atoms outside contour = 2590, contour level = 0.31205 Position of vsm_PDB.pdb (#8) relative to Vesamicol- cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) coordinates: Matrix rotation and translation -0.94874131 0.11842422 -0.29302837 244.09970759 0.18793346 0.95681279 -0.22178886 18.65504729 0.25410812 -0.26549009 -0.93002370 217.73038409 Axis -0.07898820 -0.98892703 0.12563513 Axis point 105.68249952 0.00000000 127.40186397 Rotation angle (degrees) 163.94074284 Shift along axis -10.37489195 > view matrix models > #8,-0.94874,0.11842,-0.29303,246.22,0.18793,0.95681,-0.22179,20.676,0.25411,-0.26549,-0.93002,217.19 > view matrix models > #8,-0.94874,0.11842,-0.29303,242.88,0.18793,0.95681,-0.22179,25.536,0.25411,-0.26549,-0.93002,217.82 > view matrix models > #8,-0.94874,0.11842,-0.29303,242.54,0.18793,0.95681,-0.22179,26.911,0.25411,-0.26549,-0.93002,217.88 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.94935,-0.25082,-0.18927,269.96,-0.19304,0.94083,-0.27851,74.751,0.24792,-0.22787,-0.9416,215.85 > ui mousemode right ""translate selected models"" > view matrix models > #8,-0.94935,-0.25082,-0.18927,268.11,-0.19304,0.94083,-0.27851,70.575,0.24792,-0.22787,-0.9416,215.97 > fitmap #8 inMap #7 Fit molecule vsm_PDB.pdb (#8) to map Vesamicol- cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) using 3068 atoms average map value = 0.07904, steps = 84 shifted from previous position = 3.85 rotated from previous position = 6.69 degrees atoms outside contour = 2470, contour level = 0.31205 Position of vsm_PDB.pdb (#8) relative to Vesamicol- cryosparc_P34_J1433_map_J1426flip_3.50_resampled.mrc (#7) coordinates: Matrix rotation and translation -0.96836724 -0.13735439 -0.20832344 259.30112099 -0.08221532 0.96387571 -0.25334611 52.58553585 0.23559611 -0.22820470 -0.94467830 221.11939410 Axis 0.05611462 -0.99081046 0.12306816 Axis point 118.40737724 0.00000000 128.70411903 Rotation angle (degrees) 167.05483683 Shift along axis -10.33895784 > show #!6 models > hide #!6 models > close session > open D:/183/183-map/183-0708-PDB/ACh/PDB- > load/cryosparc_P34_J1741_003_volume_map_sharp.mrc Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.932, shown at level 0.197, step 1, values float32 > open D:/183/183-map/183-0708-PDB/apo/pdb- > load/cryosparc_P34_J608_004_volume_map_sharp.mrc Opened cryosparc_P34_J608_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.932, shown at level 0.206, step 1, values float32 > open > ""D:/183/183-map/183-0708-PDB/ph=5.5/map/cryosparc_P49_J393_003_volume_map_sharp > (1).mrc"" Opened cryosparc_P49_J393_003_volume_map_sharp (1).mrc as #3, grid size 256,256,256, pixel 0.932, shown at level 0.158, step 1, values float32 > open D:/183/183-map/183-0708-PDB/vesamicol/pdb- > load/cryosparc_P34_J1433_map.mrc Opened cryosparc_P34_J1433_map.mrc as #4, grid size 256,256,256, pixel 0.832, shown at level 0.0676, step 1, values float32 > volume #1 level 0.496 > set bgColor white > volume #2 level 0.5064 > surface dust #1 size 9.32 > surface dust #2 size 9.32 > select add #2 2 models selected > view matrix models #2,1,0,0,20.482,0,1,0,-46.786,0,0,1,37.321 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.094748,0.83461,-0.54264,123.48,-0.65155,0.36014,0.66767,22.631,0.75267,0.41682,0.50966,-40.567 > view matrix models > #2,-0.86557,0.077572,-0.49474,303.35,0.14261,-0.90884,-0.39201,220.3,-0.48005,-0.40987,0.77561,175.32 > view matrix models > #2,-0.5224,-0.52055,-0.67537,358.32,0.53062,0.42154,-0.73535,56.031,0.66749,-0.74251,0.056002,170.97 > view matrix models > #2,-0.47041,-0.74359,-0.47516,352.81,0.42102,0.2841,-0.86141,102.74,0.77553,-0.60527,0.17943,124.81 > view matrix models > #2,-0.52097,-0.53275,-0.66691,358.51,0.52505,0.41601,-0.74247,58.322,0.67299,-0.73697,0.062988,168.7 > view matrix models > #2,-0.50307,-0.63615,-0.58501,358.16,0.47607,0.36097,-0.80191,78.829,0.7213,-0.68192,0.12126,148.43 > view matrix models > #2,-0.7816,-0.36302,-0.50727,348.52,0.61437,-0.58872,-0.52531,141.38,-0.10794,-0.72224,0.68317,180.29 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.7816,-0.36302,-0.50727,311.3,0.61437,-0.58872,-0.52531,175.96,-0.10794,-0.72224,0.68317,138.52 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit map cryosparc_P34_J608_004_volume_map_sharp.mrc in map cryosparc_P34_J1741_003_volume_map_sharp.mrc using 31893 points correlation = 0.9112, correlation about mean = 0.7477, overlap = 3.049e+04 steps = 196, shift = 1.76, angle = 19.9 degrees Position of cryosparc_P34_J608_004_volume_map_sharp.mrc (#2) relative to cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.83713208 -0.29889581 -0.45811698 305.77226424 0.46846477 -0.82413718 -0.31833735 197.17935390 -0.28240154 -0.48110208 0.82993383 112.33118092 Axis -0.20247587 -0.21858629 0.95458030 Axis point 143.07630505 145.10430188 0.00000000 Rotation angle (degrees) 156.30073024 Shift along axis 2.21692267 > select up 8 models selected > select up 8 models selected > select up 8 models selected > select up 8 models selected > select up 8 models selected > vop resample #2 on #1 Opened cryosparc_P34_J608_004_volume_map_sharp.mrc resampled as #5, grid size 256,256,256, pixel 0.932, shown at step 1, values float32 > select subtract #2 6 models selected > show #!3 models > select subtract #3 4 models selected > select subtract #1 2 models selected > select add #3 4 models selected > volume #3 level 0.6321 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.029785,-0.67333,-0.73874,292.35,0.74268,0.47974,-0.46721,32.197,0.66899,-0.56256,0.48578,51.695,#4,-0.029785,-0.67333,-0.73874,292.35,0.74268,0.47974,-0.46721,32.197,0.66899,-0.56256,0.48578,51.695 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.029785,-0.67333,-0.73874,284.81,0.74268,0.47974,-0.46721,27.055,0.66899,-0.56256,0.48578,59.37,#4,-0.029785,-0.67333,-0.73874,284.81,0.74268,0.47974,-0.46721,27.055,0.66899,-0.56256,0.48578,59.37 > view matrix models > #3,-0.029785,-0.67333,-0.73874,281.85,0.74268,0.47974,-0.46721,22.055,0.66899,-0.56256,0.48578,52.201,#4,-0.029785,-0.67333,-0.73874,281.85,0.74268,0.47974,-0.46721,22.055,0.66899,-0.56256,0.48578,52.201 > fitmap #3 inMap #1 Fit map cryosparc_P49_J393_003_volume_map_sharp (1).mrc in map cryosparc_P34_J1741_003_volume_map_sharp.mrc using 16359 points correlation = 0.79, correlation about mean = 0.2221, overlap = 1.446e+04 steps = 192, shift = 3.17, angle = 16.8 degrees Position of cryosparc_P49_J393_003_volume_map_sharp (1).mrc (#3) relative to cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.16852532 -0.75346085 -0.63552810 297.54505780 0.85396218 0.21040500 -0.47589740 41.19435297 0.49228835 -0.62291772 0.60796850 68.75817511 Axis -0.07466334 -0.57275445 0.81631962 Axis point 127.74312162 197.81308472 0.00000000 Rotation angle (degrees) 100.08307567 Shift along axis 10.31869008 > vop resample #3 on #1 Opened cryosparc_P49_J393_003_volume_map_sharp (1).mrc resampled as #6, grid size 256,256,256, pixel 0.932, shown at step 1, values float32 > select subtract #3 2 models selected > show #!4 models [Repeated 1 time(s)] > volume #4 level 0.1923 > surface dust #4 size 8.32 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.029785,-0.67333,-0.73874,287.41,0.74268,0.47974,-0.46721,-14.615,0.66899,-0.56256,0.48578,70.211 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.91428,-0.031959,-0.40383,277.12,-0.37323,0.45398,0.80908,-31.138,0.15747,0.89044,-0.42699,68.847 > view matrix models > #4,-0.9563,-0.034336,-0.29035,269.75,-0.26678,0.50883,0.81849,-48.825,0.11964,0.86018,-0.49576,83.149 > view matrix models > #4,-0.91672,-0.04379,-0.39712,277.9,-0.35542,0.54338,0.76054,-37.123,0.18248,0.83835,-0.51369,80.802 > view matrix models > #4,-0.93865,-0.060616,-0.33951,275.83,-0.31457,0.55402,0.77078,-43.532,0.14137,0.8303,-0.53909,88.569 > volume #4 level 0.425 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.93865,-0.060616,-0.33951,258.61,-0.31457,0.55402,0.77078,-12.394,0.14137,0.8303,-0.53909,57.353 > view matrix models > #4,-0.93865,-0.060616,-0.33951,265.15,-0.31457,0.55402,0.77078,4.0027,0.14137,0.8303,-0.53909,69.037 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.90105,0.23003,-0.3677,233.37,-0.14251,0.64368,0.75191,-21.309,0.40964,0.7299,-0.5472,52.825 > view matrix models > #4,-0.90467,0.19049,-0.38117,239.41,-0.14777,0.69878,0.69991,-21.005,0.39968,0.68951,-0.60401,64.298 > view matrix models > #4,-0.95741,0.23545,-0.1671,216.94,0.046821,0.69772,0.71484,-42.651,0.2849,0.67657,-0.67903,85.67 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.95741,0.23545,-0.1671,214.18,0.046821,0.69772,0.71484,-39.896,0.2849,0.67657,-0.67903,84.657 > fitmap #4 inMap #1 Fit map cryosparc_P34_J1433_map.mrc in map cryosparc_P34_J1741_003_volume_map_sharp.mrc using 17649 points correlation = 0.2908, correlation about mean = 0.06262, overlap = 2848 steps = 72, shift = 2.4, angle = 9.3 degrees Position of cryosparc_P34_J1433_map.mrc (#4) relative to cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.91745885 0.36902847 -0.14861776 192.17749894 0.17815932 0.71513397 0.67590137 -52.76296656 0.35570846 0.59363406 -0.72185185 90.18932965 Axis -0.15081752 -0.92456199 -0.34991312 Axis point 93.92171649 0.00000000 69.39230268 Rotation angle (degrees) 164.17274590 Shift along axis -11.75953063 > view matrix models > #4,-0.91746,0.36903,-0.14862,171.35,0.17816,0.71513,0.6759,-70.702,0.35571,0.59363,-0.72185,54.044 > view matrix models > #4,-0.91746,0.36903,-0.14862,190.65,0.17816,0.71513,0.6759,-70.254,0.35571,0.59363,-0.72185,100.94 > view matrix models > #4,-0.91746,0.36903,-0.14862,188.59,0.17816,0.71513,0.6759,-48.086,0.35571,0.59363,-0.72185,93.477 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.93434,0.12817,-0.33253,235.85,-0.082841,0.82941,0.55246,-19.879,0.34661,0.54374,-0.76434,104.32 > fitmap #4 inMap #1 Fit map cryosparc_P34_J1433_map.mrc in map cryosparc_P34_J1741_003_volume_map_sharp.mrc using 17649 points correlation = 0.2888, correlation about mean = 0.06942, overlap = 2867 steps = 76, shift = 2.61, angle = 11.9 degrees Position of cryosparc_P34_J1433_map.mrc (#4) relative to cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.95494352 -0.04967564 -0.29260076 252.06811138 -0.22095432 0.77721510 0.58916540 -2.89213908 0.19814657 0.62727108 -0.75317257 107.40790143 Axis 0.07311522 -0.94162065 -0.32864071 Axis point 118.68733729 0.00000000 72.02751855 Rotation angle (degrees) 164.89513190 Shift along axis -14.14529510 > view matrix models > #4,-0.95134,-0.13079,-0.27902,258.86,-0.24192,0.87783,0.41338,7.5809,0.19087,0.46076,-0.86676,138.16 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.95134,-0.13079,-0.27902,265.02,-0.24192,0.87783,0.41338,7.2592,0.19087,0.46076,-0.86676,139.78 > fitmap #4 inMap #1 Fit map cryosparc_P34_J1433_map.mrc in map cryosparc_P34_J1741_003_volume_map_sharp.mrc using 17649 points correlation = 0.9282, correlation about mean = 0.5568, overlap = 1.668e+04 steps = 76, shift = 1.06, angle = 10.2 degrees Position of cryosparc_P34_J1433_map.mrc (#4) relative to cryosparc_P34_J1741_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation -0.97578855 -0.12798227 -0.17736188 256.23520117 -0.17652228 0.93963163 0.29314208 6.75126103 0.12913785 0.31735301 -0.93947351 170.29463811 Axis 0.07778298 -0.98469833 -0.15594554 Axis point 121.69653961 0.00000000 94.84030557 Rotation angle (degrees) 171.04658942 Shift along axis -13.27390718 > vop resample #4 on #1 Opened cryosparc_P34_J1433_map.mrc resampled as #7, grid size 256,256,256, pixel 0.932, shown at step 1, values float32 > show #!6 models > show #!5 models > close #4 > close #3 > close #2 > hide #!1 models > hide #!7 models > hide #!6 models > save D:/183/183-map/P34_J608_004.cmap models #5 > hide #!5 models > show #!6 models > save D:/183/183-map/P49_J393_003.cmap models #6 > save D:/183/183-map/P34_J1433.cmap models #7 > hide #!6 models > show #!6 models > show #!5 models > show #!1 models > show #!7 models > open D:/183/183-map/183-0708-PDB/ACh/PDB-load/ACh.pdb Chain information for ACh.pdb #2 --- Chain | Description A | No description available > hide #!7 models > hide #!6 models > hide #!5 models > volume #1 level 0.7931 > open D:/183/183-map/183-0708-PDB/apo/pdb-load/apo-load.pdb Chain information for apo-load.pdb #3 --- Chain | Description B | No description available > select add #3 3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected > hide #!1 models > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,8.7726,0,1,0,-21.367,0,0,1,52.877 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.75698,-0.28042,0.5902,3.5159,0.22978,0.95978,0.16131,-61.552,-0.6117,0.013504,0.79097,146.02 > view matrix models > #3,0.74118,-0.28903,0.6059,4.5978,0.23509,0.95717,0.16901,-62.73,-0.62879,0.017171,0.77738,149.11 > view matrix models > #3,0.78823,-0.26995,0.553,2.844,0.21733,0.96285,0.16024,-60.346,-0.57572,-0.0061199,0.81762,141.14 > view matrix models > #3,0.53617,-0.34298,0.77129,16.139,0.29281,0.93257,0.21114,-71.294,-0.7917,0.11263,0.60044,176.76 > view matrix models > #3,0.58816,-0.33278,0.73711,12.747,0.28051,0.93878,0.19999,-69.339,-0.75854,0.089139,0.64551,170.59 > view matrix models > #3,0.5765,-0.33524,0.74516,13.484,0.28339,0.93739,0.20247,-69.789,-0.76638,0.094442,0.63541,172.01 > view matrix models > #3,0.45349,-0.35545,0.81731,22.032,0.30983,0.92271,0.22938,-74.168,-0.83567,0.14921,0.52857,185.67 > view matrix models > #3,0.252,0.42176,-0.87099,144.29,-0.19263,0.90388,0.38195,-30.734,0.94836,0.071525,0.30902,12.14 > view matrix models > #3,-0.98929,0.061172,-0.1325,247.86,-0.02639,-0.96793,-0.24983,242.22,-0.14353,-0.24366,0.95918,102.94 > view matrix models > #3,-0.79274,0.029604,-0.60884,282.5,0.095093,-0.98058,-0.1715,220.74,-0.60209,-0.19385,0.77454,171.23 > view matrix models > #3,-0.80749,0.02986,-0.58913,281.96,0.092136,-0.98008,-0.17596,221.53,-0.58265,-0.19637,0.78865,167.68 > view matrix models > #3,-0.75795,0.028801,-0.65168,283.38,0.10132,-0.9817,-0.16123,218.99,-0.6444,-0.18823,0.74116,179.26 > view matrix models > #3,-0.72146,0.027703,-0.6919,283.81,0.10688,-0.98277,-0.15079,217.29,-0.68416,-0.18274,0.70607,187.19 > hide #!2 models > show #!5 models > view matrix models > #3,-0.74726,0.028504,-0.66392,283.55,0.10304,-0.98203,-0.15813,218.48,-0.6565,-0.18658,0.73089,181.63 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.74726,0.028504,-0.66392,278.75,0.10304,-0.98203,-0.15813,229.43,-0.6565,-0.18658,0.73089,131.19 > color #3 #55aa00ff > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.74763,-0.10139,-0.65633,293.27,0.18929,-0.97982,-0.064266,208.54,-0.63657,-0.17228,0.75173,124.84 > view matrix models > #3,-0.74341,-0.12804,-0.65647,295.94,0.21334,-0.97563,-0.051306,203.79,-0.6339,-0.17819,0.75261,125.12 > view matrix models > #3,-0.81666,-0.1209,-0.56432,293.21,0.18895,-0.97993,-0.063509,208.51,-0.54532,-0.15849,0.82311,104.54 > view matrix models > #3,-0.80403,-0.14102,-0.57762,295.62,0.25877,-0.95763,-0.12641,204.86,-0.53533,-0.25111,0.80646,116.19 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.80403,-0.14102,-0.57762,296.02,0.25877,-0.95763,-0.12641,214.86,-0.53533,-0.25111,0.80646,119.09 > view matrix models > #3,-0.80403,-0.14102,-0.57762,294.47,0.25877,-0.95763,-0.12641,216.07,-0.53533,-0.25111,0.80646,118.03 > fitmap #3 inMap #5 Fit molecule apo-load.pdb (#3) to map P34_J608_004.cmap (#5) using 3044 atoms average map value = 0.8206, steps = 96 shifted from previous position = 2.15 rotated from previous position = 20.6 degrees atoms outside contour = 969, contour level = 0.50641 Position of apo-load.pdb (#3) relative to P34_J608_004.cmap (#5) coordinates: Matrix rotation and translation -0.83705225 -0.29874831 -0.45835902 305.78501903 0.46848580 -0.82409338 -0.31841981 197.18691120 -0.28260325 -0.48126870 0.82976855 112.38139756 Axis -0.20260449 -0.21866225 0.95453562 Axis point 143.09744626 145.11722752 0.00000000 Rotation angle (degrees) 156.30369810 Shift along axis 2.20129557 > save D:/183/183-map/apo_load_resample.pdb models #3 relModel #5 > hide #!3 models > hide #!5 models > open D:/183/183-map/183-0708-PDB/ph=5.5/map/VAChT-protonated-pdb-load- > coot-0.pdb Chain information for VAChT-protonated-pdb-load-coot-0.pdb #4 --- Chain | Description A | No description available > show #!6 models > select subtract #3 Nothing selected > volume #6 level 0.411 > select add #4 3037 atoms, 3113 bonds, 1 pseudobond, 404 residues, 2 models selected > view matrix models #4,1,0,0,-27.529,0,1,0,-0.11174,0,0,1,-37.184 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.62109,-0.61849,0.48138,43.099,0.15746,0.70015,0.69641,-54.599,-0.76776,-0.35673,0.53225,146.39 > view matrix models > #4,0.32015,-0.84241,0.43341,111.26,0.015235,0.46201,0.88675,-28.358,-0.94725,-0.27729,0.16074,196.65 > view matrix models > #4,0.20471,-0.063766,-0.97674,176.43,-0.90387,0.37066,-0.21363,206.55,0.37566,0.92658,0.018241,-93.059 > view matrix models > #4,0.17988,-0.082537,-0.98022,182.04,-0.9153,0.35101,-0.19753,208.64,0.36037,0.93273,-0.012405,-88.806 > view matrix models > #4,0.16446,-0.094534,-0.98184,185.51,-0.92207,0.33881,-0.18707,209.85,0.35034,0.9361,-0.031448,-86.044 > view matrix models > #4,0.13682,-0.11669,-0.9837,191.7,-0.93355,0.31693,-0.16744,211.85,0.3313,0.94124,-0.065571,-80.861 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.13682,-0.11669,-0.9837,224.98,-0.93355,0.31693,-0.16744,208.33,0.3313,0.94124,-0.065571,-30.014 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.26413,-0.1403,-0.95423,209.46,-0.83692,-0.52508,-0.15446,296.76,-0.47937,0.83941,-0.25611,99.516 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.26413,-0.1403,-0.95423,209,-0.83692,-0.52508,-0.15446,298.75,-0.47937,0.83941,-0.25611,95.697 > view matrix models > #4,0.26413,-0.1403,-0.95423,209.88,-0.83692,-0.52508,-0.15446,295.35,-0.47937,0.83941,-0.25611,96.287 > hide #!6 models > show #!2 models > view matrix models > #4,0.26413,-0.1403,-0.95423,209.65,-0.83692,-0.52508,-0.15446,295.39,-0.47937,0.83941,-0.25611,96.044 > view matrix models > #4,0.26413,-0.1403,-0.95423,225.68,-0.83692,-0.52508,-0.15446,278.34,-0.47937,0.83941,-0.25611,137.44 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.69298,-0.67158,-0.26224,333.8,0.44318,-0.10991,-0.88967,149.74,0.56866,-0.73274,0.3738,135.74 > view matrix models > #4,-0.30101,-0.8057,-0.51014,328.23,0.68458,0.18985,-0.70378,65.432,0.66388,-0.56108,0.49442,91.182 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.30101,-0.8057,-0.51014,308.58,0.68458,0.18985,-0.70378,78.098,0.66388,-0.56108,0.49442,51.289 > hide #!2 models > show #!6 models > view matrix models > #4,-0.30101,-0.8057,-0.51014,309.84,0.68458,0.18985,-0.70378,79.468,0.66388,-0.56108,0.49442,50.628 > fitmap #4 inMap #6 Fit molecule VAChT-protonated-pdb-load-coot-0.pdb (#4) to map P49_J393_003.cmap (#6) using 3037 atoms average map value = 0.1468, steps = 64 shifted from previous position = 2.47 rotated from previous position = 5.59 degrees atoms outside contour = 2510, contour level = 0.41095 Position of VAChT-protonated-pdb-load-coot-0.pdb (#4) relative to P49_J393_003.cmap (#6) coordinates: Matrix rotation and translation -0.36106779 -0.79055386 -0.49462570 312.64698351 0.61854843 0.19390506 -0.76144508 94.52474795 0.69787379 -0.58088327 0.41898299 55.24191200 Axis 0.09734919 -0.64293144 0.75971199 Axis point 107.47552857 209.00945863 0.00000000 Rotation angle (degrees) 111.96807303 Shift along axis 11.63094219 > view matrix models > #4,-0.36107,-0.79055,-0.49463,308.94,0.61855,0.19391,-0.76145,101.66,0.69787,-0.58088,0.41898,60.128 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.41125,-0.70842,-0.57361,313.22,0.662,0.20047,-0.7222,91.604,0.62661,-0.67673,0.38653,83.596 > view matrix models > #4,-0.42352,-0.6846,-0.59326,313.85,0.67645,0.19659,-0.70977,89.051,0.60253,-0.70191,0.37983,90.218 > fitmap #4 inMap #6 Fit molecule VAChT-protonated-pdb-load-coot-0.pdb (#4) to map P49_J393_003.cmap (#6) using 3037 atoms average map value = 0.5124, steps = 104 shifted from previous position = 2.75 rotated from previous position = 19.4 degrees atoms outside contour = 1293, contour level = 0.41095 Position of VAChT-protonated-pdb-load-coot-0.pdb (#4) relative to P49_J393_003.cmap (#6) coordinates: Matrix rotation and translation -0.16866597 -0.75332040 -0.63565722 297.57781562 0.85351249 0.21094551 -0.47646444 41.25930084 0.49301944 -0.62290474 0.60738906 68.72269841 Axis -0.07436999 -0.57320062 0.81603318 Axis point 127.71038967 197.91443513 0.00000000 Rotation angle (degrees) 100.08830132 Shift along axis 10.29928726 > save D:/183/183-map/VAChT-protonated-resample.pdb models #4 relModel #6 > hide #!6 models > hide #!4 models > open D:/183/183-map/183-0708-PDB/vesamicol/pdb-load/vsm_PDB-coot-0.pdb Chain information for vsm_PDB-coot-0.pdb #8 --- Chain | Description A | No description available > select subtract #4 Nothing selected > select add #8 3068 atoms, 3146 bonds, 1 pseudobond, 406 residues, 2 models selected > show #!4 models > view matrix models > #8,0.5645,0.81594,-0.12483,-32.77,-0.72929,0.42218,-0.53843,213.27,-0.38662,0.39498,0.83337,16.336 > view matrix models > #8,0.75213,-0.49354,-0.43671,134.42,-0.57138,-0.1582,-0.80529,291.58,0.32836,0.85522,-0.40098,1.6301 > view matrix models > #8,0.48994,-0.54596,-0.67962,197.47,-0.78762,0.056921,-0.61353,272.06,0.37365,0.83588,-0.40212,-1.3993 > ui mousemode right ""translate selected models"" > view matrix models > #8,0.48994,-0.54596,-0.67962,197.16,-0.78762,0.056921,-0.61353,273.23,0.37365,0.83588,-0.40212,12.425 > ui mousemode right ""rotate selected models"" > view matrix models > #8,0.47583,-0.54708,-0.68869,199.94,-0.79388,0.069922,-0.60405,271.45,0.37862,0.83416,-0.40104,11.92 > view matrix models > #8,0.55104,-0.41446,-0.72428,178.54,-0.83228,-0.33598,-0.44094,308.18,-0.060587,0.84578,-0.53008,76.921 > view matrix models > #8,0.36721,-0.55118,-0.74924,219.81,-0.92246,-0.11255,-0.36931,284.79,0.11923,0.82676,-0.54977,59.499 > view matrix models > #8,0.36426,-0.53876,-0.75964,219.74,-0.92825,-0.14417,-0.34287,286.58,0.075209,0.83003,-0.55262,64.721 > view matrix models > #8,0.40609,-0.53965,-0.73748,212.51,-0.90767,-0.14459,-0.394,289.41,0.10599,0.82938,-0.54854,60.657 > hide #!4 models > show #!4 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > view matrix models > #8,0.279,-0.77586,-0.56586,238.64,-0.93904,-0.097153,-0.32979,280.87,0.20089,0.62338,-0.75567,95.34 > view matrix models > #8,-0.049499,-0.71813,-0.69414,284.63,0.47218,0.5956,-0.64985,59.761,0.88011,-0.35993,0.30961,21.901 > view matrix models > #8,-0.094297,-0.73324,-0.6734,289.73,0.68114,0.44579,-0.58079,45.424,0.72605,-0.51345,0.4574,43.794 > hide #!4 models > show #!7 models > fitmap #8 inMap #7 Fit molecule vsm_PDB-coot-0.pdb (#8) to map P34_J1433.cmap (#7) using 3068 atoms average map value = 0.4144, steps = 96 shifted from previous position = 1.65 rotated from previous position = 17.1 degrees atoms outside contour = 1606, contour level = 0.42499 Position of vsm_PDB-coot-0.pdb (#8) relative to P34_J1433.cmap (#7) coordinates: Matrix rotation and translation -0.17401543 -0.74994712 -0.63819899 298.12375422 0.84629354 0.21747116 -0.48630601 42.23979286 0.50349366 -0.62472843 0.59683206 68.71960439 Axis -0.07035855 -0.58030948 0.81135109 Axis point 127.27727137 199.24167051 0.00000000 Rotation angle (degrees) 100.36137848 Shift along axis 10.26801754 > save D:/183/183-map/183-0708-PDB/vsm_resample.pdb models #8 relModel #7 > show #!6 models > show #!5 models > show #!4 models > show #!3 models > show #!2 models > show #!1 models > surface dust #1 size 9.32 > surface dust #5 size 9.32 > surface dust #6 size 9.32 > surface dust #7 size 9.32 > hide #!1 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!8 models > select subtract #8 Nothing selected > hide #!4 models > hide #!3 models > select ::name=""ACH"" 10 atoms, 9 bonds, 1 residue, 1 model selected > color sel cyan > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:25-478 3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected > color (#!2 & sel) dark gray > hide sel atoms > select #2/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel #ff00ffff > color sel #ff39ffff > color sel #c02effff > color sel #ffffffff > color sel #ff00ffff > color sel #dd35ffff > color sel #b73cffff > color sel #ffffffff > color sel #ff00ffff > color sel #ce39ffff > color sel #b633e2ff > color sel #a62eceff > color sel #ce39ffff > color sel #a62eceff > select #2/A:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:396 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:396 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/A:394-395 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:394-395 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff7fff > color sel #a62eceff > select #2/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #a62eceff > show #!3 models > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #3/B Alignment identifier is 3/B > select #3/B:25-26 17 atoms, 16 bonds, 2 residues, 1 model selected > select #3/B 3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected > color (#!3 & sel) dark gray > select #3/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel #ffffffff > color sel #6449ffff > color sel #7a46ffff > color sel #8b3dffff > color sel #a639ffff > color sel #9c22ffff > color sel #8018ffff > color sel #790bffff > color sel #8331ffff > color sel #9b54ffff > color sel #9c75ffff > color sel #ffffffff > color sel #6449ffff > color sel #4520ffff > color sel #430affff > color sel #4208ffff > color sel #a66affff > color sel #896cffff > color sel #6f71ffff > color sel #aaff00ff > color sel #6f71ffff > select #3/B:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #3/B:398-399 15 atoms, 14 bonds, 2 residues, 1 model selected > select #3/B:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #6f71ffff > select #3/B:428-429 18 atoms, 18 bonds, 2 residues, 1 model selected > select #3/B:428-429 18 atoms, 18 bonds, 2 residues, 1 model selected > select #3/B:428-429 18 atoms, 18 bonds, 2 residues, 1 model selected > select #3/B:428-429 18 atoms, 18 bonds, 2 residues, 1 model selected > select #3/B:426 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:426-427 14 atoms, 13 bonds, 2 residues, 1 model selected > select > #3/B:28-60,122-147,152-171,176-203,207-236,244-263,268-273,282-287,289-308,312-319,324-328,333-351,356-376,380-411,418-445,448-460,463-468 2385 atoms, 2425 bonds, 321 residues, 1 model selected > select #3/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #3/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #6f71ffff > hide #!3 models > show #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > select #4/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A 3037 atoms, 3113 bonds, 1 pseudobond, 404 residues, 2 models selected > color (#!4 & sel) dark gray > select #4/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel #c8bb2dff > color sel #b6a829ff > color sel #aaff00ff > color sel #b6a829ff > select #4/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select #4/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #b6a829ff > select #4/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #4/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #b6a829ff > hide #!4 models > show #!8 models > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > select #8/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:25-478 3049 atoms, 3125 bonds, 1 pseudobond, 405 residues, 2 models selected > color (#!8 & sel) dark gray > hide sel atoms > select #8/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel #5ba33bff > select #8/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #5ba33bff > select #8/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > color sel #aaff00ff > color sel #5ba33bff > hide #!8 models > cartoon style width 0.7 > transparency 60 cartoons > show #!2 models > show #!3 models > show #!4 models > show #!8 models > ui tool show ""Side View"" > hide #!8 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > hide #!6 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!3 models > lighting soft > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > show #!1 models > ui tool show ""Color Zone"" > color zone #1 near #2 distance 5.59 > volume splitbyzone #1 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 0 as #9.1, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 1 as #9.2, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 2 as #9.3, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 Opened cryosparc_P34_J1741_003_volume_map_sharp.mrc 3 as #9.4, grid size 256,256,256, pixel 0.932, shown at level 0.793, step 1, values float32 > hide #!9 models > hide #!9.1 models > hide #!9.2 models > show #!9 models > hide #!9.4 models > volume #9.3 style mesh > volume #9.3 level 0.5616 > transparency #2#9.3#!9 50 > transparency #2#9.3#!9 80 > transparency #2#9.3#!9 20 > select ::name=""ACH"" 10 atoms, 9 bonds, 1 residue, 1 model selected > color sel byhetero > color #9.3 #0000ffcc models > color #9.3 #ffffffcc models > color #9.3 blue models > color #9.3 #6e61ffff models > color #9.3 #868cffff models > color #9.3 #a4b0ffff models > color #9.3 #c1c7ffff models > color #9.3 #a1aaffff models > color #9.3 white models > color #9.3 #5500ffff models > color #9.3 #777effff models > color #9.3 #8e8effff models > color #9.3 black models > color #9.3 #5153c8ff models > color #9.3 #858fc8ff models > color #9.3 #cce4f7ff models > color #9.3 #ffaaffff models > color #9.3 white models > color #9.3 #aaaaffff models > color #9.3 #4cc8a9ff models > color #9.3 #4e5ec8ff models > volume #9.3 style surface > volume #9.3 style mesh > hide #!9.3 models > show #!9.3 models > hide #!9.3 models > show #!9.3 models > hide #!9.3 models > show #!3 models > show #!9.3 models > hide #!9.3 models > hide #!3 models > show #!9.3 models > hide #!9.3 models > ui mousemode right distance > distance #2/A:428@OH #2/A:398@OD1 Distance between ACh.pdb #2/A TYR 428 OH and ASP 398 OD1: 2.654Å > hide #10.1 models > show #!9.3 models > hide #!9.3 models > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:476-478 24 atoms, 23 bonds, 3 residues, 1 model selected > select #2/A:25-478 3044 atoms, 3120 bonds, 2 pseudobonds, 404 residues, 3 models selected > color (#!2 & sel) byhetero > select #2/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > show #!9.3 models > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > save D:/183/Fig-12/ach-d425-soft-1.png width 2000 height 2000 supersample 4 > transparentBackground true > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > lighting full > lighting shadows false > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > save D:/183/Fig-12/ach-d425-soft-1.png width 2000 height 2000 supersample 4 > transparentBackground true > transparency sel 0 > transparency sel 100 > transparency sel 0 > lighting soft > lighting full > lighting flat > lighting full > lighting soft > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > lighting full > volume #9.3 style surface > transparency sel 60 > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > volume #9.3 style mesh > lighting full > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > lighting full > lighting shadows false > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > lighting soft [Repeated 1 time(s)] > lighting full > lighting shadows false > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > lighting soft > lighting full > lighting shadows false > lighting soft > lighting shadows true intensity 0.5 > save D:/183/Fig-12/1.png width 2000 height 2000 supersample 4 > transparentBackground true > lighting full > lighting shadows false > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > volume #9.3 color #ff55ff > volume #9.3 color #55aaff > volume #9.3 color blue > lighting full > lighting shadows false > save D:/183/Fig-12/ChimeraX/398-ach.png width 2000 height 2000 supersample 4 > transparentBackground true > hide #!10 models > hide #!9.3 models > close #10 > show #!3 models > show #!5 models > hide #!2 models > show #!2 models > color zone #5 near #3 distance 5.59 > volume splitbyzone #5 Opened P34_J608_004.cmap 0 as #10.1, grid size 256,256,256, pixel 0.932, shown at level 0.506, step 1, values float32 Opened P34_J608_004.cmap 1 as #10.2, grid size 256,256,256, pixel 0.932, shown at level 0.506, step 1, values float32 Opened P34_J608_004.cmap 2 as #10.3, grid size 256,256,256, pixel 0.932, shown at level 0.506, step 1, values float32 > volume #10.3 style mesh > hide #!2 models > volume #10.3 level 0.362 > color #3#10.3#!9-10 byhetero > save D:/183/Fig-12/ChimeraX/398-apo.png width 2000 height 2000 supersample 4 > transparentBackground true > hide #!3 models > show #!4 models > show #!6 models > color zone #6 near #4 distance 5.59 > volume splitbyzone #6 Opened P49_J393_003.cmap 0 as #11.1, grid size 256,256,256, pixel 0.932, shown at level 0.411, step 1, values float32 Opened P49_J393_003.cmap 1 as #11.2, grid size 256,256,256, pixel 0.932, shown at level 0.411, step 1, values float32 Opened P49_J393_003.cmap 2 as #11.3, grid size 256,256,256, pixel 0.932, shown at level 0.411, step 1, values float32 > hide #!9 models > hide #!10 models > hide #!11 models > show #!11 models > hide #!11.1 models > hide #!11.2 models > volume #11.3 level 0.2013 > volume #11.3 style mesh > color #4#11.3#!11 byhetero > save D:/183/Fig-12/ChimeraX/398-5.5.png width 2000 height 2000 supersample 4 > transparentBackground true > hide #!11 models > hide #!11.3 models > hide #!4 models > show #!8 models > show #!7 models > color zone #7 near #8 distance 5.59 > hide #!8 models > hide #!7 models > show #!6 models > hide #!6 models > show #!11.3 models > show #!4 models > color #11.3 #4e5ec8ff models > save D:/183/Fig-12/ChimeraX/398-5.5.png width 2000 height 2000 supersample 4 > transparentBackground true > hide #!11 models > hide #!11.3 models > hide #!4 models > show #!8 models > show #!7 models > hide #!7 models > show #!10.1 models > hide #!10.1 models > show #!10.3 models > hide #!10.3 models > hide #!10 models > hide #7.1 models > show #7.1 models > color zone #7 near #8 distance 5.59 > volume splitbyzone #7 Opened P34_J1433.cmap 0 as #12.1, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 1 as #12.2, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 2 as #12.3, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 3 as #12.4, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 4 as #12.5, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 5 as #12.6, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 > hide #!12.1 models > hide #!12.2 models > hide #!12.5 models > hide #!12.6 models > select ::name=""VSM"" 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel yellow > color zone #7 near #8 distance 5.59 > volume splitbyzone #7 Opened P34_J1433.cmap 0 as #13.1, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 1 as #13.2, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 2 as #13.3, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 Opened P34_J1433.cmap 3 as #13.4, grid size 256,256,256, pixel 0.932, shown at level 0.425, step 1, values float32 > hide #!13.1 models > hide #!13.2 models > hide #!12.4 models > hide #!12.3 models > volume #13.3 level 0.1573 > volume #13.4 > volume #13.3 style mesh > color sel byhetero > ui tool show ""Show Sequence Viewer"" > sequence chain #8/A Alignment identifier is 8/A > select #8/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel byhetero > color sel byelement > ui mousemode right select > select #8/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel byhetero > select #8/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel byhetero > select #8/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:130-131 15 atoms, 14 bonds, 2 residues, 1 model selected > select #8/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > volume #13.3 color #4e5ec8 > select #8/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:478 6 atoms, 5 bonds, 1 residue, 1 model selected > save D:/183/Fig-12/ChimeraX/398-VSM.png width 2000 height 2000 supersample 4 > transparentBackground true > ui mousemode right distance > distance #8/A:428@OH #8/A:131@NZ Distance between vsm_PDB-coot-0.pdb #8/A TYR 428 OH and LYS 131 NZ: 2.877Å > hide #14.1 models > save D:/183/Fig-12/ChimeraX/398-VSM.png width 2000 height 2000 supersample 4 > transparentBackground true > save D:/183/Fig-12/ChimeraX/D398.cxs includeMaps true ——— End of log from Wed Dec 11 15:01:23 2024 ——— opened ChimeraX session > hide #!13.3 models > show #!13.3 models > hide #!13.3 models > show #!13.3 models > show #!13.4 models > hide #!13.4 models > show #!13.2 models > hide #!13.2 models > show #!13.2 models > hide #!13.2 models > show #!13.2 models > hide #!13.2 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > ui tool show Distances Exactly two atoms must be selected! > ui mousemode right select > select clear > ui mousemode right translate > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > ui tool show ""Hide Dust"" > surface dust #13.3 size 5.59 > surface dust #13.3 size 6.06 > surface dust #13.3 size 1.51 > ui tool show Distances > distance style radius 0.2 > distance style radius 0.15 > hide #!13.3 models > show #!13.3 models > hide #!13.3 models > show #!13.3 models > hide #!13.3 models > show #!13.3 models > hide #!13.3 models > show #!13.3 models > show #!13.1 models > hide #!13 models > hide #!13.1 models > show #!13.2 models > hide #!13.2 models > hide #!13.3 models > show #!13.3 models > hide #!13 models > show #!12.5 models > hide #!12.5 models > show #!12.6 models > hide #!12.6 models > show #!12.4 models > hide #!12.4 models > show #!12.3 models > hide #!12.3 models > show #!12.3 models > hide #!12.3 models > show #!12.2 models > hide #!12.2 models > show #!12.1 models > hide #!12.1 models > hide #!12 models > show #!12 models > close #12 > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > rename #13 ""VSM_P34_J1433.cmap split"" > show #!11 models > hide #!11 models > show #!11 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > volume #11.3 level 0.1415 > hide #!14 models > show #!14 models > hide #!14 models > hide #!8 models > show #!4 models > volume #11.3 level 0.1938 > surface dust #11.3 size 5.59 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > rename #11 ""PRO_P49_J393_003.cmap split"" > hide #!11 models > show #!10.3 models > rename #10 ""APO_P34_J608_004.cmap split"" > hide #!4 models > show #!3 models > color #10.3 #5869cfff models > hide #!10.3 models > show #!10.3 models > hide #!10.3 models > show #!10.3 models > hide #!10.3 models > show #!10.3 models > hide #!10.3 models > show #!10.3 models > hide #!10.3 models > show #!10.3 models > surface dust #10.3 size 5.59 > volume #10.3 level 0.2697 > hide #!10 models > show #!9 models > show #!9.3 models > color #9.3 #6374d5ff models > hide #!3 models > show #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > rename #9 ""ACh——cryosparc_P34_J1741_003_volume_map_sharp.mrc split"" > rename #9 ""ACh_cryosparc_P34_J1741_003_volume_map_sharp.mrc split"" > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!9 models > hide #!4 models > hide #!3 models > hide #!2 models > show #!7 models > hide #!7 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!6 models > hide #!6 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!2 models > show #!3 models > show #!4 models > ui mousemode right select > hide #!4 models > hide #!3 models > open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT- > zw/183_structure/VAChT-ACh/VAChT-ACh.pdb Chain information for VAChT-ACh.pdb #12 --- Chain | Description A | No description available Computing secondary structure > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > select add #12 3054 atoms, 3129 bonds, 1 pseudobond, 405 residues, 2 models selected > select subtract #12 Nothing selected > hide #!2 models > select #12/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > show #!2 models > hide #!2 models > show #!2 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > select add #12 3054 atoms, 3129 bonds, 1 pseudobond, 405 residues, 2 models selected > select subtract #12 Nothing selected > hide #!12 models > show #!12 models > close #12 > open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT- > zw/183_structure/VAChT-apo/VAChT-apo.pdb Chain information for VAChT-apo.pdb #12 --- Chain | Description B | No description available Computing secondary structure > hide #!2 models > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select add #12 3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected > show sel atoms > select subtract #12 Nothing selected > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > close #3 > select add #12 3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected > hide sel atoms > select subtract #12 Nothing selected > hide #!2 models > select #12/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select #12/B:425 8 atoms, 7 bonds, 1 residue, 1 model selected > select #12/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #12/B:425 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select clear > show #!2 models > hide #!2 models > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!2 models > hide #!2 models > select #12/B:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > show #!2 models > hide #!2 models > hide #!12 models > show #!12 models > show #!4 models > hide #!4 models > color #12 #a99e2aff > color #12 #a9a92aff > color #12 darkgrey > show #!2 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!2 models > hide #2.1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select add #12 3044 atoms, 3120 bonds, 1 pseudobond, 404 residues, 2 models selected > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > undo > hide #!12 models > show #!2 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > color #12 #a9a9a981 > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > color #12 #d8d8d8ff > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > color #12 #d8d8d895 > color #12 #d8d8d858 > color #12 #d8d8d868 > color #12 #d8d8d867 > color #12 #d8d8d866 > select clear > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > cartoon style width 1 > hide #!2 models > show #!2 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > color #12 #d8d8d8fa > color #12 #d8d8d8ff > color #12 #d8d8d8dc > color #12 #d8d8d8ff > color #12 #d8d8d8ec > color #12 #d8d8d8cb > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color #12 #ebebebff > color #12 #ebebebc5 > color #12 #ebebebcd > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!2 models > show #!2 models > show #!12 models > color #12 #b2b2b2ff > color #12 #b2b2b278 > color #12 #b2b2b280 > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!2 models > show #!12 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel #b2b2b280 > color sel #70b2b280 > color sel #7090b280 > color sel #7090dd80 > color sel #7090dd81 > color sel #7090dd86 > color sel #7090dd8f > color sel #7090dd99 > color sel #7090dd9a > color sel #7090dda7 > color sel #7090ddb2 > color sel #7090ddba > color sel #7090ddc2 > color sel #7090ddc7 > color sel #7090ddcd > color sel #7090ddd5 > color sel #7090dddc > color sel #7090ddde > color sel #7090dde1 > color sel #7090dde2 > color sel #7090dde5 > color sel #7090dde7 > color sel #7090dded > color sel #7090ddf2 > color sel #7090ddf5 > color sel #7090ddf7 > color sel #7090ddf8 > color sel #7090ddfa > color sel #7090ddfb > color sel #7090ddfc > color sel #7090ddfd > color sel #7090ddfe > color sel #7090ddff > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel #7090ddff > color sel byhetero > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel #7090ddff > color sel byhetero > select clear > show #!10 models > hide #!10 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > select #12/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #12/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #12/B:131 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > select #12/B:428@CZ 1 atom, 1 residue, 1 model selected > select clear > select down 1 bond, 1 model selected > select down 1 bond, 1 model selected > select down 1 bond, 1 model selected > select #12/B:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > hide #!12 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > show #!12 models > transparency 50 cartoons > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!12 models > show #!4 models > hide #!4 models > show #!4 models > open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT- > zw/183_structure/VAChT-protonated/VAChT-protonated.pdb Chain information for VAChT-protonated.pdb #3 --- Chain | Description A | No description available > hide #!4 models > show #!4 models > select add #3 3037 atoms, 3112 bonds, 1 pseudobond, 404 residues, 2 models selected > show sel atoms > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide sel atoms > select subtract #3 Nothing selected > hide #!4 models > select #3/A:131 9 atoms, 8 bonds, 1 residue, 1 model selected > show #!4 models > hide #!4 models > select #3/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > show #!4 models > hide #!4 models > select #3/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!4 models > hide #!4 models > select add #3/A:428 20 atoms, 19 bonds, 2 residues, 1 model selected > show #!4 models > hide #!4 models > select add #3/A:131 29 atoms, 27 bonds, 3 residues, 1 model selected > color #3 #b2b2b2ff > color #3 #b2b2b280 > show sel atoms > color sel #f3c27880 > color sel #f3c27881 > color sel #f3c27883 > color sel #f3c27885 > color sel #f3c27887 > color sel #f3c27890 > color sel #f3c2789a > color sel #f3c278a2 > color sel #f3c278af > color sel #f3c278be > color sel #f3c278ca > color sel #f3c278cf > color sel #f3c278d4 > color sel #f3c278d9 > color sel #f3c278e4 > color sel #f3c278e8 > color sel #f3c278ee > color sel #f3c278f4 > color sel #f3c278fc > color sel #f3c278ff > color sel byhetero > select clear > transparency 50 cartoons > cartoon style width 1 > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!5 models > hide #!5 models > show #!6 models > volume #6 level 0.1902 > ui tool show ""Color Zone"" > color zone #6 near #3 distance 5.44 > color zone #6 near #3 distance 38.72 > color zone #6 near #3 distance 14.77 > color zone #6 near #3 distance 27.91 > color zone #6 near #3 distance 30.01 > color zone #6 near #3 distance 87.72 > hide #!6 models > select #3/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/A:428 20 atoms, 19 bonds, 2 residues, 1 model selected > select add #3/A:131 29 atoms, 27 bonds, 3 residues, 1 model selected > color sel #f3c278ff > show #!6 models > color zone #6 near #3 distance 87.72 > ui tool show ""Side View"" > color zone #6 near #3 distance 96.1 > color zone #6 near #3 distance 175.03 > color zone #6 near #3 distance 195.22 > color zone #6 near #3 distance 411.35 > color zone #6 near #3 distance 396.57 > color zone #6 near #3 distance 932 > volume splitbyzone #6 Opened P49_J393_003.cmap 0 as #15.1, grid size 256,256,256, pixel 0.932, shown at level 0.19, step 1, values float32 Opened P49_J393_003.cmap 1 as #15.2, grid size 256,256,256, pixel 0.932, shown at level 0.19, step 1, values float32 Opened P49_J393_003.cmap 2 as #15.3, grid size 256,256,256, pixel 0.932, shown at level 0.19, step 1, values float32 > hide #!15.1 models > hide #!15.2 models > volume #15.3 style mesh > select clear > volume #15.3 level 0.1341 > volume #15.3 color #5869cf > volume #15.3 level 0.2089 > select #3/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/A:428 20 atoms, 19 bonds, 2 residues, 1 model selected > select add #3/A:131 29 atoms, 27 bonds, 3 residues, 1 model selected > color sel byhetero > select clear > transparency 50 cartoons > select clear > surface dust #15.2 size 5.59 > surface dust #15.2 size 5.86 > surface dust #15.2 size 6.37 > surface dust #15.3 size 5.59 > transparency 80 mesh Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 80 surfaces > transparency 90 surfaces > transparency 10 surfaces > transparency 30 surfaces > hide #!3 models > show #!3 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > close #4 > show #!8 models > hide #!15 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > open /Users/feiwenwei/Documents/fdu/lab/18/183/0506-VAChT- > zw/183_structure/VAChT-VSM/VAChT-VSM.pdb Chain information for VAChT-VSM.pdb #4 --- Chain | Description A | No description available Computing secondary structure > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > select #4/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > select add #4/A:131 21 atoms, 20 bonds, 2 residues, 1 model selected > show sel atoms > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!7 models > hide #!7 models > show #!8 models > show #!13 models > volume #13.3 level 0.1776 > volume #13.3 level 0.1857 > hide #!13 models > hide #!8 models > show #!8 models > hide #!8 models > select clear > select add #4 3070 atoms, 3148 bonds, 1 pseudobond, 406 residues, 2 models selected > hide sel atoms > select ::name=""VSM"" 38 atoms, 42 bonds, 2 residues, 2 models selected > select clear > select ::name=""VSM"" 38 atoms, 42 bonds, 2 residues, 2 models selected > show sel & #!4 atoms > color (#!4 & sel) yellow > color (#!4 & sel) byhetero > select clear > color #4 #bbbbbbff > color #4 #bbbbbb80 > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 21 bonds, 1 residue, 1 model selected > color sel yellow > color sel #bbbbbb80 > color sel #bbbbbb86 > color sel #bbbbbba6 > color sel #bbbbbbb0 > color sel #bbbbbbb7 > color sel #bbbbbbc0 > color sel #bbbbbbca > color sel #bbbbbbcb > color sel #bbbbbbd6 > color sel #bbbbbbe1 > color sel #bbbbbbf0 > color sel #bbbbbbff > color sel #fffb00ff > color sel byhetero > select clear > cartoon style width 1 > show #!8 models > hide #!8 models > select #4/A:398 8 atoms, 7 bonds, 1 residue, 1 model selected > show #!8 models > hide #!8 models > select add #4/A:428 20 atoms, 19 bonds, 2 residues, 1 model selected > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > select add #4/A:131 29 atoms, 27 bonds, 3 residues, 1 model selected > show sel atoms > color sel #fffb00ff > color sel #68d587ff > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > color sel byhetero > select clear > transparency 50 cartoons > select clear > show #!8 models > hide #!8 models > show #!8 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!8 models > show #!8 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!15 models > hide #!15 models > rename #15 ""PROP49_J393_003.cmap split"" > rename #15 ""PRO_P49_J393_003.cmap split"" > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!13 models > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/250515_D398.cxs > includeMaps true > ui tool show ""Side View"" > lighting soft > lighting simple > lighting full > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting simple > lighting full > hide #!8 models > hide #!13 models > show #!15 models > show #!3 models > hide #!3 models > hide #!15 models > show #!12 models > show #!10 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #!13 models > show #!4 models > hide #!12 models > hide #!10 models > hide #!4 models > show #!2 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > surface dust #9.3 size 5.59 > hide #!9 models > hide #!2 models > show #!3 models > show #!15 models > hide #!15 models > show #!15 models > hide #!15 models > hide #!3 models > show #!13 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!13 models > show #!10 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!10 models > show #!15 models > show #!3 models > hide #!3 models > show #!3 models > hide #!15 models > hide #!3 models > show #!12 models > show #!10 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > ui tool show Distances > select #12/B:428@OH 1 atom, 1 residue, 1 model selected > select add #12/B:398@OD1 2 atoms, 2 residues, 1 model selected > distance #12/B:428@OH #12/B:398@OD1 Distance between VAChT-apo.pdb #12/B TYR 428 OH and ASP 398 OD1: 2.655Å > distance #12/B:428@OH #12/B:398@OD1 Distance already exists; modify distance properties with 'distance style' > distance style symbol false > distance style symbol true > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > distance style symbol false > distance style symbol true > distance style symbol false > distance style symbol true > distance style symbol false > distance style symbol true > distance style symbol false > distance style dashes 8 > distance style decimalPlaces 2 > distance style decimalPlaces 3 > distance style dashes 9 > distance style radius 0.1 > distance style symbol true > distance style decimalPlaces 2 > distance style dashes 10 > distance style dashes 9 > distance style dashes 8 > distance style dashes 7 > distance style radius 0.15 > stick width 1 Unknown command: stick width 1 > style stick thick 1 Expected a keyword > style stick ringFill thick 1 Expected a keyword > style stick ringFill thick 2 Expected a keyword > style stick ringFill thick Changed 15273 atom styles, 2025 residue ring styles > style stick ringFill thick dashes 2 Changed 15273 atom styles, 6 pseudobond dashes, 2025 residue ring styles > undo > size stickRadius 2 Changed 15655 bond radii > size stickRadius 1 Changed 15655 bond radii > size stickRadius 0.5 Changed 15655 bond radii > size stickRadius 0.3 Changed 15655 bond radii > select clear > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/250515_D398.cxs > includeMaps true > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398APO.png > width 1341 height 1019 supersample 3 transparentBackground true > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398APO.png > width 1000 height 1000 supersample 3 transparentBackground true > hide #!14 models > hide #!12 models > hide #!10 models > show #!14 models > hide #!14 models > show #!4 models > show #!13 models > show #!14 models > hide #!14 models > show #!14 models > select #4/A:131@NZ 1 atom, 1 residue, 1 model selected > select add #4/A:428@OH 2 atoms, 2 residues, 1 model selected > distance #4/A:131@NZ #4/A:428@OH Distance between VAChT-VSM.pdb #4/A LYS 131 NZ and TYR 428 OH: 2.88Å > select clear > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png > width 1000 height 1000 supersample 3 transparentBackground true > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png > width 500 height 500 supersample 3 transparentBackground true > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png > width 500 height 500 supersample 1 transparentBackground true > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM.png > width 500 height 500 supersample 3 transparentBackground true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > save > /Users/feiwenwei/Documents/fdu/lab/18/183/manuscripts&Figs/Figs/20250512/Fig5/D398VSM_nomiaobian.png > width 1000 height 1000 supersample 3 transparentBackground true > volume #13.3 style surface > volume #13.3 style mesh > volume #13.3 style surface > volume #13.3 color #4e5ec81f > volume #13.3 color #4e5ec800 > volume #13.3 color #4e5ec832 > select #4/A:428 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel #4e5ec833 > color sel #4e5ec83c > color sel #4e5ec8b5 > color sel #4e5ec8b8 > color sel #4e5ec8b9 > color sel #4e5ec8c0 > color sel #4e5ec8c3 > color sel #4e5ec8ca > color sel #4e5ec8cc > color sel #4e5ec8ce > color sel #4e5ec8cf > color sel #4e5ec8d0 > color sel #4e5ec8d1 > color sel #4e5ec8d2 > color sel #4e5ec8d3 > color sel #4e5ec8d4 > color sel #4e5ec8d5 > color sel #4e5ec8d6 > color sel #4e5ec8d7 > color sel #4e5ec8d8 > color sel #4e5ec8d9 > color sel #4e5ec8e2 > color sel #4e5ec8f0 > color sel #4e5ec8f7 > color sel #4e5ec8fa > color sel #4e5ec8fb > color sel #4e5ec8ff > undo > color sel #68d587ff > color sel byhetero > select clear > color #4 #ebebebff > color #4 #d6d6d6ff > undo > select #13.3 2 models selected > select clear > select #4/A:131@NZ 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 11 atoms, 9 bonds, 2 residues, 1 model selected > color sel #d6d6d6ff > color sel #68d587ff > color sel byhetero > select clear > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/feiwenwei/Downloads/emd_38652.map Opened emd_38652.map as #1, grid size 256,256,256, pixel 0.85, shown at level 0.414, step 1, values float32 OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGR3CH/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 3天5小时52分钟 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2719D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX